Not to speak for AT, but while an injury is coming back other muscles and structures are over loading to compensate. If the original injury doesn't get back to 100%, which is rare with many injuries, the body is always compensating. So compensatory injuries happen. All those surrounding muscles & structures become more likely to failure.
I'm sure CnD will correct me if I bastardized what I've tried to learn from him.
I agree 100% with your post. My point was just that not all injuries are interconnected, sometimes bad things just happen, especially when you look at the forces that are applied to the body during a football game.
This is also why I mentioned the versaclimber for conditioning purposes vs running, if you had data on how fast guys can actually run, whether its timed runs or GPS data, you would have something to compare post injury performance to and have a better idea of when they are actually recovered. To be fair, they might do this, Ill have to ask around